For StarTrix , you get EQS and then wait like 2 months or something.

There are two methods to bring up the Equestrian Resistance storyline. The first, as LoveDueT stated, is to wait two months after the Conquest of Equestria for the storyline to kick in.

The second option is to form the Manehatten Protectorate. Ensure that you don't try to squash the resurgence levels as long as possible. During play as the Protectorate, there will be prompts to where the Equestrian Resistance will try to destabilize the area. If you do not bring any troops into those territories and pick the option to stabilize the area in 60 days, that territory will fall under control of the rebels.

As more territories are "destabilized", you'll eventually receive a prompt stating that the situation is getting out of control and that no more territories must be lost. This is the point where the ELF (Equestrian Liberation Front) is nearly ready to mobilize and start trying to reclaim Equestria. Simply lose one more territory and you will be given one last prompt to choose between playing as the Protectorate or the ELF. Pick the ELF and you are good to go.